OXA-48 Carbapenemase-Encoding Transferable Plasmids of Klebsiella pneumoniae Recovered from Egyptian Patients Suffering from Complicated Urinary Tract Infections
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Collection of Clinical Isolates
2.2. Antimicrobial Susceptibility of the Collected Isolates
2.3. Phenotypic Detection of CPs
2.3.1. Blue-Carba Test
2.3.2. Modified Carbapenem Inactivation Method (mCIM)
2.3.3. EDTA-Modified Carbapenem Inactivation Method (eCIM)
2.4. Phenotypic Analysis Using Heatmap Signature
2.5. Molecular Detection of Plasmid-Borne Carbapenemase Genes
2.5.1. Extraction of Plasmid DNA from Carbapenem-Resistant Isolates
2.5.2. Amplification of Some Plasmid-Encoded Carbapenemase Genes
2.5.3. Sequencing of PCR Products
2.5.4. Transformation
2.6. Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR) for Isolates Containing Plasmids
2.7. Statistical Analysis
3. Results
3.1. Collection of Clinical Isolates
3.2. Identification of the Collected GNB Clinical Isolates
3.3. Antimicrobial Susceptibility of the Collected Isolates
3.4. Phenotypic Detection of CPs
3.5. Extraction of Plasmid DNA and Amplification of Carbapenemase Genes
3.6. Transformation of Plasmids into Competent E. coli DH5α
3.7. Genotyping of CR-GNB Containing Plasmids
3.8. Statistical Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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PCR Reaction | Gene | Primer | Primer Sequence (5′ → 3′) | Expected PCR Product Size (bp) | Ta (°C) | References |
---|---|---|---|---|---|---|
Multiplex | blaKPC | Pf | TGTCACTGTATCGCCGTC | 1011 | 50 | [28] |
Pr | CTCAGTGCTCTACAGAAAACC | |||||
blaNDM | Pf | GGTTTGGCGATCTGGTTTTC | 621 | [29,30] | ||
Pr | CGGAATGGCTCATCACGAT | |||||
Multiplex | blaVIM | Pf | TCTACATGACCGCGTCTGTC | 748 | 50 | [31] |
Pr | TGTGCTTTGACAACGTTCGC | |||||
blaOXA-48 | Pf | GCGTGGTTAAGGATGAACAC | 438 | [28,30] | ||
Pr | CATCAAGTTCAACCCAACCG | |||||
Monoplex | blaIMP | Pf | CTACCGCAGCAGAGTCTTTG | 587 | 50 | [32] |
Pr | AACCAGTTTTGCCTTACCAT | |||||
Multiplex | aac(6′)-Ib | Pf | TTGCGATGCTCTATGAGTGG | 358 | 49 | [33] |
Pr | CGTTTGGATCTTGGTGACCT | |||||
blaSHV | Pf | GGTTATGCGTTATATTCGCC | 867 | [34] | ||
Pr | TTAGCGTTGCCAGTGCTC | |||||
Multiplex | blaCTX-M | Pf | CGCTTTGCGATGTGCAG | 550 | 51 | [35] |
Pr | ACCGCGATATCGTTGGT | |||||
blaTEM | Pf | ATGAGTATTCAACATTTCCG | 867 | [34] | ||
Pr | CTGACAGTTACCAATGCTTA | |||||
ERIC-PCR | Pf | AAGTAAGTGACTGGGGTGAGCG | Variable | 45 | [36] | |
Pr | ATGTAAGCTCCTGGGGATTCAC |
PCR Reaction | Primary Denaturation | Secondary Denaturation | Annealing | Extension | No. of Cycles | Final Extension |
---|---|---|---|---|---|---|
Multiplex blaKPC/blaNDM | 95 °C 4 min | 95 °C 30 s | 50 °C 45 s | 72 °C 1 min | 30 | 72 °C 10 min |
Multiplex blaVIM/blaOXA-48 | 95 °C 4 min | 95 °C 30 s | 50 °C 45 s | 72 °C 1 min | 30 | 72 °C 10 min |
Monoplex blaIMP | 95 °C 4 min | 95 °C 30 s | 50 °C 45 s | 72 °C 1 min | 30 | 72 °C 10 min |
Multiplex aac(6′)-Ib/blaSHV | 95 °C 4 min | 95 °C 30 s | 49 °C 45 s | 72 °C 1 min | 30 | 72 °C 10 min |
Multiplex blaCTX-M/blaTEM | 95 °C 4 min | 95 °C 30 s | 51 °C 45 s | 72 °C 1 min | 30 | 72 °C 10 min |
ERIC-PCR | 95 °C 15 min | 94 °C 30 s | 45 °C 45 s | 72 °C 7 min | 45 | 72 °C 10 min |
Antimicrobial Class | Antimicrobial Agent | Percentage of Resistance (%) | |||||
---|---|---|---|---|---|---|---|
Klebsiella spp. (n = 28) | P. aeruginosa (n = 19) | A. baumannii (n = 8) | E. coli (n = 6) | Proteus mirabilis (n = 2) | Enterobacter cloacae (n = 2) | ||
Carbapenems | Imipenem (10 µg) | 64.3 | 89.5 | 100 | 33.3 | 50 | 0 |
Meropenem (10 µg) | 71.4 | 94.7 | 87.5 | 16.7 | 50 | 0 | |
Ertapenem (10 µg) | 92.9 | ND | ND | 100 | 100 | 100 | |
Doripenem (10 µg) | 46.4 | 42.1 | 25 | 16.7 | 50 | 0 | |
β-lactam combination agents | Amoxicillin/clavulanic acid (30 µg) | 46.4 | ND | ND | 16.7 | 50 | 0 |
Ampicillin/sulbactam (20 µg) | 89.3 | ND | 25 | 50 | 50 | 50 | |
Cephalosporins | Cefoxitin (30 µg) | 89.3 | ND | ND | 83.3 | 50 | 50 |
Ceftazidime (30 µg) | 85.7 | 94.7 | 87.5 | 100 | 50 | 100 | |
Ceftriaxone (30 µg) | 89.3 | ND | 87.5 | 100 | 50 | 100 | |
Cefepime (30 µg) | 78.6 | 78.9 | 87.5 | 100 | 50 | 50 | |
Aminoglycosides | Amikacin (30 µg) | 78.6 | 47.4 | 100 | 0 | 50 | 0 |
Gentamicin (10 µg) | 64.3 | 89.5 | 100 | 0 | 50 | 100 | |
Fluoroquinolones | Ciprofloxacin (5 µg) | 92.9 | 100 | 100 | 100 | 100 | 100 |
Levofloxacin (5 µg) | 92.9 | 100 | 62.5 | 100 | 50 | 100 | |
Folate pathway inhibitors | Trimethoprim/sulfamethoxazole (25 µg) | 78.6 | ND | 50 | 100 | 100 | 100 |
Nitrofurans | Nitrofurantoin (300 µg) | 92.9 | ND | ND | 0 | 0 | 0 |
Fosfomycins | Fosfomycin (200 µg) | 10.7 | ND | ND | 0 | 0 | 50 |
Tested Isolates | Blue-Carba Test (n = 65) [26] | Modified Carbapenem Inactivation Method (mCIM) (n = 57) [25] | EDTA-Modified Carbapenem Inactivation Method (eCIM) (n = 29) [25] | |||
---|---|---|---|---|---|---|
No. of CPs/Total No. of Tested Isolates | % | No. of CPs/Total No. of Tested Isolates | % | No. of MBL Producers/Total No. of Tested Isolates | % | |
Klebsiella spp. | 22/28 | 78.6 | 23/28 | 82.1 | 12/23 | 52.2 |
P. aeruginosa | 7/19 | 36.8 | 2/19 | 10.5 | ND | ND |
A. baumannii | 1/8 | 12.5 | ND | ND | ND | ND |
E. coli | 3/6 | 50 | 4/6 | 66.7 | 3/4 | 75 |
Proteus mirabilis | 2/2 | 100 | 1/2 | 50 | 0/1 | 0 |
Enterobacter cloacae | 1/2 | 50 | 1/2 | 50 | 1/1 | 100 |
TS24.SK | 24.SK | TS37.AK | 37.AK | TS59.WK | 59.WK | TS66.WK | 66.WK | E. coli DH5α | |
---|---|---|---|---|---|---|---|---|---|
Antimicrobial susceptibility testing | |||||||||
Imipenem (10 µg) | I | I | I | R | I | R | I | I | S |
Meropenem (10 µg) | R | R | S | R | S | R | S | R | S |
Ertapenem (10 µg) | R | R | S | R | S | R | S | R | S |
Doripenem (10 µg) | S | I | S | S | S | R | S | R | S |
Amoxicillin/clavulanic acid (30 µg) | S | R | S | S | S | R | S | I | S |
Ampicillin/sulbactam (20 µg) | R | R | R | R | R | R | R | R | S |
Cefoxitin (30 µg) | R | R | R | R | R | R | R | R | S |
Ceftazidime (30 µg) | R | R | R | R | R | R | R | R | S |
Ceftriaxone (30 µg) | I | I | I | R | I | R | R | R | S |
Cefepime (30 µg) | SDD | SDD | S | R | S | R | SDD | R | S |
Amikacin (30 µg) | S | S | S | R | S | R | S | R | S |
Gentamicin (10 µg) | S | S | S | R | S | R | S | S | S |
Ciprofloxacin (5 µg) | R | R | S | R | S | R | S | R | S |
Levofloxacin (5 µg) | R | R | S | R | S | R | S | R | S |
Trimethoprim/sulfamethoxazole (25 µg) | S | S | S | R | S | R | S | R | S |
Nitrofurantoin (300 µg) | S | R | S | S | S | R | S | R | S |
Fosfomycin (200 µg) | S | S | S | R | S | S | S | S | S |
Blue-Carba test | |||||||||
+ | + | + | + | + | + | + | + | - | |
Modified carbapenem inactivation method (mCIM) | |||||||||
+ | + | + | + | + | + | + | + | - |
Parental Strain | Transformant Code | Plasmid Code | Acquired Transformant Phenotype | Plasmid Genotype | Plasmid Size in Gel | |
---|---|---|---|---|---|---|
24.SK | TS24.SK | pKPT24 | Imipenem (10 µg) | I | blaOXA-48/blaCTX-M | 2 plasmid bands: Large plasmid: >10 kb Small plasmid: ≈1700 bp |
Meropenem (10 µg) | R | |||||
Ertapenem (10 µg) | R | |||||
Ampicillin/sulbactam (20 µg) | R | |||||
Cefoxitin (30 µg) | R | |||||
Ceftazidime (30 µg) | R | |||||
Ceftriaxone (30 µg) | I | |||||
Cefepime (30 µg) | SDD | |||||
Ciprofloxacin (5 µg) | R | |||||
Levofloxacin (5 µg) | R | |||||
37.AK | TS37.AK | pKPT37 | Imipenem (10 µg) | I | blaOXA-48 | 2 plasmid bands: Large plasmid: >10 kb Small plasmid: >10 kb |
Ampicillin/sulbactam (20 µg) | R | |||||
Cefoxitin (30 µg) | R | |||||
Ceftazidime (30 µg) | R | |||||
Ceftriaxone (30 µg) | I | |||||
59.WK | TS59.WK | pKPT59 | Imipenem (10 µg) | I | blaOXA-48/blaTEM/blaaac(6′)-Ib | 1 plasmid band: >10 kb |
Ampicillin/sulbactam (20 µg) | R | |||||
Cefoxitin (30 µg) | R | |||||
Ceftazidime (30 µg) | R | |||||
Ceftriaxone (30 µg) | I | |||||
66.WK | TS66.WK | pKPT66 | Imipenem (10 µg) | I | blaOXA-48/blaCTX-M | 1 plasmid band: >10 kb |
Ampicillin/sulbactam (20 µg) | R | |||||
Cefoxitin (30 µg) | R | |||||
Ceftazidime (30 µg) | R | |||||
Ceftriaxone (30 µg) | R | |||||
Cefepime (30 µg) | SDD |
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Elshamy, A.A.; Saleh, S.E.; Alshahrani, M.Y.; Aboshanab, K.M.; Aboulwafa, M.M.; Hassouna, N.A. OXA-48 Carbapenemase-Encoding Transferable Plasmids of Klebsiella pneumoniae Recovered from Egyptian Patients Suffering from Complicated Urinary Tract Infections. Biology 2021, 10, 889. https://doi.org/10.3390/biology10090889
Elshamy AA, Saleh SE, Alshahrani MY, Aboshanab KM, Aboulwafa MM, Hassouna NA. OXA-48 Carbapenemase-Encoding Transferable Plasmids of Klebsiella pneumoniae Recovered from Egyptian Patients Suffering from Complicated Urinary Tract Infections. Biology. 2021; 10(9):889. https://doi.org/10.3390/biology10090889
Chicago/Turabian StyleElshamy, Ann A., Sarra E. Saleh, Mohammad Y. Alshahrani, Khaled M. Aboshanab, Mohammad M. Aboulwafa, and Nadia A. Hassouna. 2021. "OXA-48 Carbapenemase-Encoding Transferable Plasmids of Klebsiella pneumoniae Recovered from Egyptian Patients Suffering from Complicated Urinary Tract Infections" Biology 10, no. 9: 889. https://doi.org/10.3390/biology10090889
APA StyleElshamy, A. A., Saleh, S. E., Alshahrani, M. Y., Aboshanab, K. M., Aboulwafa, M. M., & Hassouna, N. A. (2021). OXA-48 Carbapenemase-Encoding Transferable Plasmids of Klebsiella pneumoniae Recovered from Egyptian Patients Suffering from Complicated Urinary Tract Infections. Biology, 10(9), 889. https://doi.org/10.3390/biology10090889